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    <tr><td style="border:0px;text-align:center"><h1>myKaryoView </h1><h3>Personalized Genome Search</h3></td></tr>
      
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    <h1><a name="top">Adding data using easyDAS</a></h1>
      <h2>Contents</h2>
      <ul>
        <li><a href="#data_file">1 - Before we begin...</a></li>
        <li><a href="#register">2 - Accessing easyDAS</a></li>

        <li><a href="#upload">3 - Upload your data</a></li>
        <li><a href="#filetype">4 - Check the filetyp</a></li>
        <li><a href="#source">5 - Describe your source</a></li>
        <li><a href="#coordinates">6 - Assign a coordinate system</a></li>
		<li><a href="#data_type">7 - Assign Data Types</a></li>
		<li><a href="#paste_url">8 - Paste Private URL in myKaryoView </a></li>
		<li><a href="#config_source">9 - Configure Created Source </a></li>
		<li><a href="#corolary">10 - A Word of Caution </a></li>
      </ul>
	  
	  
     <h1>Adding data using easyDAS</h1>
      <p>You can use easyDAS to publish annotations on biological sequences. Actual data can come from files in different <a href="http://wwwdev.ebi.ac.uk/panda-srv/easydas/documentation/formats.html">formats</a>, with GFF files being more strict on sintax and semantics but a bit easier to use and tabular files offering more freedom.</p>

      <p>This tutorial will show how to create a data source with a tabular file. It is very easy to create a tabular file with a spreadsheet program (MS Excel, OpenOffice Calc, etc...) or even by hand. For the tutorial we will use <a href="http://wwwdev.ebi.ac.uk/panda-srv/easydas/documentation/examples/chr16.txt" target="_blank">this example data file (chr16.txt)</a> as reference.</p>

      <h2>Creating a data Source</h2>
        <h3><a name="data_file">1 - Before we begin</a></h3>
        <p> The fist thing you'll need is a data file. You can ownload <a href="http://wwwdev.ebi.ac.uk/panda-srv/easydas/documentation/examples/chr16.txt" target="_blank">the example data file (chr16.txt)</a> and save it in your machine or use any other one in a <a href="http://wwwdev.ebi.ac.uk/panda-srv/easydas/documentation/formats.html">valid format</a>.
        </p>

        <h3><a name="register">2 - Accessing easyDAS</a></h3>
          <p>Go to <a href="http://www.ebi.ac.uk/panda-srv/easydas/" target="_blank">http://www.ebi.ac.uk/panda-srv/easydas/</a>. This is the main page of easyDAS. Here you can see a list of public sources available, some of them with links to Ensembl and other browsers.</p>
          <p><strong>OPTIONAL</strong> Login or register clicking on "Login" on the top right corner of the screen. Sources created by registered users are not automatically removed and can be modified later. Anonymous users can't create private sources.</p>

        <h3><a name="upload">3 - Upload your data</a></h3>

          <p>easyDAS has a wizard to FAQ you when creating a new data source. It will guide you throug a serie of simple dialogs requesting all the needed information. To start it, click on the "Create a new source" button, on the top right corner of the the screen.</p> 
          <p>The first step in creating a new source is uploading the data file to the system. Click on "Browse" and select your data file (in this case, chr16.txt). The "Upload" button will become active. Click on it and wait for the file to be loaded. When it's done, click on "Next" to move to the next step.</p>
        
        <h3><a name="filetype">4 - Check the filetype</a></h3>
          <p>Once the file has been uploaded, easyDAS analyses it a tries to guess its format. In this second dialog, it says what has guessed and how your file looks like with the selected format. You can change the file format and its parameters if needed. If you are using a tabular file with another separator, for example "comma" instead of "tab", you can change it here.</p>
          <p>If you are using chr16.txt you can see that it has detected it's a tabular file, separated by tabs, with four columns for line. You can see the first 5 lines of data in the table. When the data in the table reflects the data in your file, click on "Next".</p>
  
        <h3><a name="source">5 - Describe your source</a></h3>

          <p>In this step, you will have to describe your new source. Assign it a name, a description, the email of the person in charge of it (possibly you), a page where to find more information about the data contained on the source, etc.. you'll find a detailed description of each field moving the mouse over the small question mark next to it. As for the last item, Coordinate System, it will be explained with more detail in the next section.</p>

        <h3><a name="coordinates">6 - Assign a coordinate system</a></h3>
          <p>Please select NCBI_36,Chromsome, Homo Sapiens.</p>
		  <p>Click "Next"</p>
		  
		<h3><a name="data_type">7 - Assign Data Types</h3>
          <p>Now you need to tell easyDAS what each column of your 23andMe data is. 
		  This is the way you need to assign data types to each column:</p>
          <ul><li>First column: select Identifier from menu</li>
              <li>Second column: Segment Id (this means chromsome)</li>
              <li>Third column: Start; then click "add" and select "End" (the SNP position is both start and end. See attached figure)</li>
              <li>Fourth colum: selectType Id</li>
          </ul>
         <p>Click "Finish"</p>

         <p>Your 23andMe data source will be created and a series of urls are produced.</p>
		 
         <h2>Displaying Source in myKaryoView</h2>
		 
		 <h3><a name="paste_url">8 - Paste created URL in myKaryoView</h3>
           <p>One of them is the feature command:</p>
			<pre>
			Features Command: http://www.ebi.ac.uk/das-srv/easydas/easy/das/test/features?segment=16:544555,554555
			</pre>
		<p>This is the one you need for entering your data source into myKaryoView.</p>

        <p>Back into myKaryoView (<a href="http://mykaryoview.com/">http://mykaryoview.com/</a>):</p>

        <p>Click on "add your data"</p>

        <h3><a name="config_source">9 - Configure Created Source</h3>
        <p>Give a name to your data source (e.g. "My Source")</p>

        <p>Take the "URL" from the "Features Command" result in easyDAS and paste it the up to the question mark</p> 
		  <p>Using the above example it would look like this:</p>
			<pre>
			http://www.ebi.ac.uk/das-srv/easydas/easy/das/test/features
			</pre>
            <p>Add a description (e.g. My 23andMe data source)</p>

        <p>Click "add source"</p>

        <p>Now your new source should be added to the table.</p>

        <p>Search by SNP, gene name, etc.</p> 
		    <p>Just "Submit Query" in the search box with the appropriate SNP id or gene name selecting it from the drop down menu. Of course, you can also search by location e.g., 1:1000000,2000000.</p>
			
	   <h3><a name="disclaimer">10 - A Word of Caution</h3>		
	   <p>myKaryoView is a prototype which is still in development. We are very keen on people to give us feedback and help us develop it if they want to. You can download the source code and modify it freely. Please <a href="credits.html">contact us</a> if you need any more instructions. 
       <p>myKaryoView does not remember your added source once you refresh the home page or go back and it does not remember the source that you added.</p>
		  
		  
		  
		  
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